Getting a grip on Covid-19 test samples

In early 2020, the world of pathology and infectious disease testing has been thrown into chaos by the Covid-19 pandemic. One of the key challenges in the global testing programmes for Covid-19 is how to track very large numbers of patient samples passing through inexperienced or under-staffed laboratories that are now being asked to increase their daily throughput by as much as 10 times their normal workload.

Over the last 20 years sample management has totally changed from its origins in the laboratory that were quite basic and rudimentary. In the beginning, clinical sample management worked by storing the samples in tubes. At this time many labs, even in large hospitals and pharmaceutical companies, stored their tubes in standard chest freezers either unlabelled or at best with handwritten labels on the rack or on the outside of the storage tube. If a clinical lab was particularly advanced, their samples might have a barcode, a 1D barcode, labelled on to the side of the rack. The databases of samples stored, if they existed, were quite often just Word documents or Excel documents, although patient samples in Pathology were tracked more effectively from the start.
更先进的样品管理是在二维条码管问世后才真正开始的。我们今天已经发展到复杂的管和样品跟踪应用。样本管理现在被认为是一门真正的、严肃的学科，因为各组织意识到他们的样本非常有价值。
The biggest issue for sample tracking during the current crisis is the availability of suitable consumables, followed by the available instruments for testing. With countries in Europe looking to test 100,000 samples per day it is not hard to see why. If a lab uses 96-well PCR plates for this testing they will need over a 1000 plates per day. Typically, these are sold in cases of 100 plates so that’s 10 cases per day, 50 cases per week. If all 27 EU states did that it would be 1350 cases of PCR plates per week. Now add in the USA and Canada, Australia, South East Asia… trying to mould, sterilise, pack and ship that many plates, even distributed across, say, 10 different manufacturers is a major logistical problem. Add to that the liquid handling tips and the RT-PCR and RNA extraction reagents which are also in short supply and the scale of the problem becomes apparent. There are now shortages of the very 2D-barcoded tubes which are so desperately needed to help track large numbers of samples.
In the short-term, if 2D-barcoded tubes are not available, the next best option is to use linear barcodes. These can be laser printed or inkjet printed onto tubes for short-term disposable use, but perhaps the quickest way to use them is a print-and-apply self-adhesive label. Two key suppliers in the lab field are Brady labels and Computype. Both can offer the printers, software to design the label and the consumables. Typically, a sample receipt form should be generated and attached to this should be multiple copies of a unique barcode on labels. This allows for bothy the documents and the tubes to carry identical copies of the bar code and for samples to be split further downstream.
为了达到某种水平的高通量，样品可以被分组成固体聚丙烯块或深井微孔板，每个容纳96孔。这些可以有一个线性条形码标签应用于一端或一侧，可以在大多数可用的自动化平台上读取，但重要的是，在一批中的所有板都有条形码应用于同一端或侧板相对于A1位置。这将防止钢板在机器人甲板上以错误的方式装载。由于其在农业生物、化合物储存、生物合成和样品储存等方面的广泛应用，目前还不缺乏2ml深井储存板。这些技术可以与96孔滤板技术(如Millpore、Waters和Porvair Sciences提供的技术)一起用于RNA清理步骤。另外，如果液体搬运机器人配备了磁珠分离技术，也可以使用磁珠分离技术。仍然需要转移到96孔PCR板，尽管384孔PCR板也可以用于加快吞吐量，如果使用的液体处理可以支持这样小的等分。所有这些块和板都可以携带一维线性条码标签。在板内跟踪样品依赖于A-H, 1-8井位坐标被准确记录;比2D条形码小瓶更少的防错性，但更便宜，目前更容易设置。
The issue of RT-PCR reagents is a thorny one, as is the RNA extraction kit. Currently, the Francis Crick Institute in the UK is testing using home-made reagents reverse-engineered from proprietary solutions by Qiagen, Merck and Roche. This can be risky and obviously, there are no quality controls or manufacturers’ guarantees that it will work in the same way that an off-the-shelf kit should. However, the Crick Covid-19 Consortium have published their SOPs for these tests on their website https://www.crick.ac.uk/research/covid-19/covid19-consortium which are optimised for Hamilton Star and Starlet robots for the clean up and Beckman FX robots for the extraction. These would need to be adapted to any other robot in use (Tecan / Perkin Elmer / Agilent etc) or smaller pipetting station (Fortitude, Eppendorf etc.) in order to replicate the Crick Covid-19 Consortium protocol. Although the Francis Crick Institute already had 2D-barcode rack scanners from Ziath and others, they were hampered by the lack of available tubes.
The Covid-19 testing protocol followed by the Francis Crick Institute involves collection of sample swabs at hospital sites in 15ml Falcon tubes. The swabs are then transferred to uncoded 2ml screw cap plastic vials and linear barcodes received with the sample from each hospital are applied to these, such that the robot’s 1D linear bar code readers can scan them on the deck. For less sophisticated automation, it should be possible to use commercially available wired, wireless or Bluetooth linear scanners such as those from Opticon for this step. The robot then transfers the digested contents of each 2ml vial to one well of a 2ml deep well plate which is already bar-coded on the short edge.
Of course, all that vital sample location data needs to be entered into a LIMS or database of some sort so that the RT-PCR results can be tied directly to the correct patient samples. There are many systems and software available for this. One of the simplest and most cost-effective is the Samples software from Ziath. This basic ‘What is it?, where is it?’ programme is an easy-to-use relational database that can be customised to track samples by any number of user-defined tracking tags, making it easy to find. For example, ‘all patients with positive RT-PCR result, over 50, who live in Cambridge, UK’. More sophisticated and highly-secure programmes such as that from ModulBio are available at a higher cost, but can take commensurately longer to acquire, install and acquire competence to use.
These are some of the ways that Sample Management issues are and will be tackled during the Covid-19 crisis and into the future. You can keep up to date with Neil Benn’s thoughts on this subject via his blog posts on the Ziath website at http://ziath.com/index.php/blog

The Authors

Neil Benn是英国剑桥Ziath公司的总经理。它已经有近15年的历史，专注于样品管理的仪器。他们的主要产品范围是与二维条码扫描仪的管在机架。他们也有样品管理软件和工具来跟踪、挑选和选择试管。Stephen Knight是Ziath的商务总监，在科学仪器和消耗品方面拥有超过30年的经验。